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- PDB-2ivx: Crystal structure of human cyclin T2 at 1.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 2ivx
TitleCrystal structure of human cyclin T2 at 1.8 A resolution
ComponentsCYCLIN-T2
KeywordsNUCLEAR PROTEIN / TRANSCRIPTION REGULATION / CELL DIVISION / PHOSPHORYLATION / CYCLIN / CELL CYCLE / TRANSCRIPTION
Function / homology
Function and homology information


early viral transcription / late viral transcription / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / host-mediated activation of viral transcription / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation ...early viral transcription / late viral transcription / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase activator activity / host-mediated activation of viral transcription / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Formation of HIV elongation complex in the absence of HIV Tat / skeletal muscle tissue development / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / transcription coactivator binding / transcription by RNA polymerase II / cell division / chromatin binding / protein kinase binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / : / 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-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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDebreczeni, J.E. / Bullock, A.N. / Fedorov, O. / Savitsky, P. / Berridge, G. / Das, S. / Pike, A.C.W. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. ...Debreczeni, J.E. / Bullock, A.N. / Fedorov, O. / Savitsky, P. / Berridge, G. / Das, S. / Pike, A.C.W. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. / Gorrec, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S.
CitationJournal: EMBO J. / Year: 2008
Title: The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.
Authors: Baumli, S. / Lolli, G. / Lowe, E.D. / Troiani, S. / Rusconi, L. / Bullock, A.N. / Debreczeni, J.E. / Knapp, S. / Johnson, L.N.
History
DepositionJun 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / struct / Item: _audit_author.name / _struct.title
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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-T2
B: CYCLIN-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0198
Polymers59,6472
Non-polymers3726
Water5,891327
1
A: CYCLIN-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0725
Polymers29,8231
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYCLIN-T2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9483
Polymers29,8231
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.032, 58.636, 65.634
Angle α, β, γ (deg.)110.63, 102.41, 90.12
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99991, -0.00938, -0.01004), (-0.00936, 0.99995, -0.0028), (0.01007, -0.00271, -0.99995)
Vector: -4.80372, -6.16668, 89.48531)

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Components

#1: Protein CYCLIN-T2 / HUMAN CYCLIN T2 / CYCT2


Mass: 29823.418 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-263 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: O60583
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 130 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 130 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, GLN 130 TO ARG ENGINEERED RESIDUE IN CHAIN B, GLN 130 TO ARG REGULATORY SUBUNIT OF THE CYCLIN-DEPENDENT KINASE PAIR (CDK9/CYCLIN T) COMPLEX, ALSO CALLED POSITIVE TRANSCRIPTION ELONGATION FACTOR B (P-TEFB), WHICH IS PROPOSED TO FACILITATE THE TRANSITION FROM ABORTIVE TO PRODUCTION ELONGATION BY PHOSPHORYLATING THE CTD (CARBOXY-TERMINAL DOMAIN) OF THE LARGE SUBUNIT OF RNA POLYMERASE II (RNAP II).

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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: 2.79 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.2M NA-FORMATE, 0.1M BIS-TRIS-PROPANE PH 8.5, 20%PEG3350, 10% ETHYLENE GLYCOL, 150 NL SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→41.86 Å / Num. obs: 53530 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.57 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.31
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.36 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→59.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.022 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1702 3.2 %RANDOM
Rwork0.191 ---
obs0.192 51982 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20.28 Å20.54 Å2
2--0.36 Å20.23 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 24 327 4440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224241
X-RAY DIFFRACTIONr_bond_other_d0.0010.022811
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9355767
X-RAY DIFFRACTIONr_angle_other_deg0.90336880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7515521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81724.074189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
X-RAY DIFFRACTIONr_nbd_refined0.2140.2933
X-RAY DIFFRACTIONr_nbd_other0.1710.22778
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22111
X-RAY DIFFRACTIONr_nbtor_other0.0840.21885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.52699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95424204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67731809
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4674.51557
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 116
Rwork0.25 3502
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)
12.0564-0.3399-0.02342.4670.282.4529-0.04650.08930.1699-0.24930.0139-0.1877-0.09080.14690.0326-0.1134-0.02160.0037-0.09760.0248-0.1586-13.833729.599555.2825
22.64031.7257-1.27153.2177-1.36781.74870.1008-0.2169-0.00530.1522-0.133-0.0858-0.00450.0330.0322-0.1160.0055-0.012-0.09660.0183-0.1298-22.523814.090573.4968
32.13430.10540.04762.5397-0.3432.0888-0.079-0.16210.00160.23510.04380.2652-0.0361-0.16850.0352-0.12640.02380.0113-0.0808-0.0075-0.14948.231223.448433.8842
42.7256-1.7432-1.14783.35781.30591.73590.1060.237-0.1055-0.1934-0.14570.190.0025-0.07130.0396-0.1089-0.0139-0.0188-0.1033-0.0342-0.087116.58968.043115.5345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 150
2X-RAY DIFFRACTION2A151 - 262
3X-RAY DIFFRACTION3B9 - 150
4X-RAY DIFFRACTION4B151 - 263

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