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- PDB-2w2h: Structural basis of transcription activation by the Cyclin T1-Tat... -

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Basic information

Entry
Database: PDB / ID: 2w2h
TitleStructural basis of transcription activation by the Cyclin T1-Tat-TAR RNA complex from EIAV
Components
  • 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'
  • CYCLIN-T1
  • PROTEIN TAT
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / TAR / TAT / CYCLIN / NUCLEUS / ACTIVATOR / CYCLIN T1 / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION / CELL CYCLE / RNA-BINDING / ACETYLATION / COILED COIL / TRANSCRIPTION / CELL DIVISION / CRYSTALLIZATION
Function / homology
Function and homology information


P-TEFb complex / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / RNA-binding transcription regulator activity / positive regulation of transcription elongation by RNA polymerase II / molecular condensate scaffold activity ...P-TEFb complex / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / host cell nucleolus / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation of DNA-templated transcription, elongation / RNA-binding transcription regulator activity / positive regulation of transcription elongation by RNA polymerase II / molecular condensate scaffold activity / cell division / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus
Similarity search - Function
Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like ...Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Protein Tat / Cyclin-T1
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
EQUINE INFECTIOUS ANEMIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsAnand, K. / Geyer, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural Insights Into the Cyclin T1-Tat-Tar RNA Transcription Activation Complex from Eiav.
Authors: Anand, K. / Schulte, A. / Vogel-Bachmayr, K. / Scheffzek, K. / Geyer, M.
History
DepositionOct 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-T1
B: CYCLIN-T1
C: PROTEIN TAT
D: PROTEIN TAT
R: 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'
S: 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8378
Polymers82,7276
Non-polymers1102
Water1086
1
A: CYCLIN-T1
C: PROTEIN TAT
R: 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4745
Polymers41,3643
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-16.57 kcal/mol
Surface area19250 Å2
MethodPISA
2
B: CYCLIN-T1
D: PROTEIN TAT
S: 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)41,3643
Polymers41,3643
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14.44 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.460, 149.460, 129.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 10:25 OR RESSEQ 27:32 OR RESSEQ...
211CHAIN B AND (RESSEQ 10:25 OR RESSEQ 27:32 OR RESSEQ...
112CHAIN C AND (RESSEQ 41:47 OR RESSEQ 49:69 )
212CHAIN D AND (RESSEQ 41:47 OR RESSEQ 49:69 )

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.0005, -1, 0.0094), (-1, -0.0006, -0.0034), (0.0035, -0.0094, -0.9999)
Vector: 127.072, -30.924, -52.0008)

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Components

#1: Protein CYCLIN-T1 / CYCT1 / CYCLIN-T


Mass: 30843.354 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-267
Source method: isolated from a genetically manipulated source
Details: GENBANK\: AF137509 / Source: (gene. exp.) EQUUS CABALLUS (horse) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9XT26
#2: Protein/peptide PROTEIN TAT / CYCLIN T1-TAT FUSION PROTEIN / TRANSACTIVATING REGULATORY PROTEIN / ETAT / E-TAT


Mass: 3493.091 Da / Num. of mol.: 2
Fragment: CYCLIN BOX DOMAIN OF EQUINE CYCLIN T1, RESIDUES 47-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUINE INFECTIOUS ANEMIA VIRUS / Strain: PGEX-4T1 / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20920
#3: RNA chain 5'-R(*GP*CP*UP*CP*AP*GP*AP*UP*CP*UP *GP*CP*GP*GP*UP*CP*UP*GP*AP*GP*C)-3' / TAR RNA


Mass: 7027.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PURIFIED SINGLE-STRANDED DNA OLIGONUCLEOTIDES / Source: (synth.) EQUINE INFECTIOUS ANEMIA VIRUS
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCYCLIN T1- TAT IS FUSION COMPLEX. MUTATION IN NUCLEOTIDE CHAINS R AND S (A3G, U24C)

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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: 2.9 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.4
Details: 7% PEG 8000, 0.1M HEPES PH7.4 0.1 M AMMONIUM SULPHATE, 15 MM MNCL2, 5% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.25→30 Å / Num. obs: 22461 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 103.83 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.74
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 8.74 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PK2

2pk2


Resolution: 3.25→29.927 Å / SU ML: 0.46 / σ(F): 1.41 / Phase error: 30.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 1191 5.3 %
Rwork0.2432 --
obs0.2451 22461 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.396 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso mean: 137.69 Å2
Baniso -1Baniso -2Baniso -3
1--9.9007 Å2-0 Å20 Å2
2---9.9007 Å2-0 Å2
3---16.5753 Å2
Refinement stepCycle: LAST / Resolution: 3.25→29.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 936 2 6 5593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145797
X-RAY DIFFRACTIONf_angle_d2.2118091
X-RAY DIFFRACTIONf_dihedral_angle_d23.1352145
X-RAY DIFFRACTIONf_chiral_restr0.167962
X-RAY DIFFRACTIONf_plane_restr0.009868
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1787X-RAY DIFFRACTIONPOSITIONAL
12B1787X-RAY DIFFRACTIONPOSITIONAL0.038
21C222X-RAY DIFFRACTIONPOSITIONAL
22D222X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2504-3.38040.38781300.37392319X-RAY DIFFRACTION100
3.3804-3.5340.39151330.3562380X-RAY DIFFRACTION100
3.534-3.720.34821320.31982348X-RAY DIFFRACTION100
3.72-3.95260.32321320.29212359X-RAY DIFFRACTION100
3.9526-4.2570.29181310.23932356X-RAY DIFFRACTION100
4.257-4.68390.23481320.2172347X-RAY DIFFRACTION100
4.6839-5.35830.22661330.19392389X-RAY DIFFRACTION100
5.3583-6.73820.25711330.22912369X-RAY DIFFRACTION100
6.7382-29.9280.24351350.19932403X-RAY DIFFRACTION99
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)
15.3007-0.3156-0.4274.8268-0.27072.22960.43350.16110.8815-0.4275-0.1102-0.1711-0.8918-0.2813-0.33090.60090.03380.29190.26780.16940.186784.8001-32.1792-28.9901
23.5186-0.2785-0.18484.4855-0.13712.3997-0.0794-0.4737-0.360.11060.35350.6189-0.3782-0.869-0.28780.70160.03550.12521.06740.29550.5577106.8467-10.0864-64.6619
31.04420.079-0.60352.9823-0.01021.16360.58250.6136-0.14430.654-0.4254-0.7693-0.2954-0.4491-0.3121.09820.38130.40470.99180.25491.26791.9655-55.4824-37.4012
44.36310.51230.521.0455-0.20540.7660.111.236-0.2620.64260.3307-0.5729-0.0971-0.4128-0.55430.91410.33440.29641.10520.28261.0615130.2074-17.3016-55.914
51.3405-0.61-0.19331.6990.32390.53450.1805-0.70711.257-0.3761-0.3929-1.92560.29551.0352-0.05820.96370.11670.50621.04580.36321.8958105.2406-52.2116-41.5486
61.7176-0.52050.37520.6056-0.11560.8036-0.5591-0.3287-1.9504-0.2880.14730.81990.82610.16790.06470.96590.11780.45010.91030.53171.9471126.9318-30.3955-51.5327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN R
6X-RAY DIFFRACTION6CHAIN S

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